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stxmjh / interproscan

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Feature request: accept stdin #14

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi guys

In order to facilitate our mpi jobs:
Would it be possible to allow interproscan.sh accept STDIN and write to STDOUT 
(for single file format e.g. -o -)? I guess it would still write the STDIN as a 
temporary fasta file (like it does with normal input).

For single file format I guess we can use the XML to produce any of the other 
formats ?
(is there a protocol for that?)

many thanks
alexie

Original issue reported on code.google.com by alpa...@gmail.com on 11 Feb 2013 at 12:15

GoogleCodeExporter commented 9 years ago 
Hi Alexie,
Thank you very much for using InterProScan 5.

I can imagine what you try to achieve. My guess is you would like to integrate 
InterProScan into your pipeline and you want to pass the STDOUT to your next 
step. You could in theory hack the bash script (interproscan.sh) to make usage 
of STDIN, but I am afraid InterProScan 5 is not able to write to STDOUT as it 
is configured at the moment. But we will discuss your point internally. In 
theory it should be possible, but only by expanding/changing the code.

That's true in theory you could use the XML file to convert it into any other 
format of your interested. But there are limitations, for instance XML result 
file you've got from a nucleotide sequence analysis you can only convert into 
GFF3 as it contains trace back information as well.
Unfortunately there is no mode in InterProScan 5 integrated at the moment you 
can run to convert XML files, but we will discuss that point internally as well.

Kind regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 19 Feb 2013 at 11:33

GoogleCodeExporter commented 9 years ago 
I'll handle this one.

Original comment by nuka....@gmail.com on 6 Aug 2013 at 4:07

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 May 2014 at 9:11

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 May 2014 at 9:13